- phenixbb - phenix-online.org

rosetta.run_tests crash
by wtempel 24 Oct '19

24 Oct '19

Hi, has anyone tried the combination of phenix-1.17 and rosetta-2019.40? Crashes in my hands, crash log attached. I may have modified the phenix installation by phenix.python -m pip install readline, in case it matters. Any suggestions appreciated. Many thanks in advance. Wolfram Tempel

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Yeast microtubule model
by Sebastiano Pasqualato 24 Oct '19

24 Oct '19

Dear all, I’m addressing to people working in the microtubule field. Has someone created, or knows where I could find, a pdb file of the yeast microtubule, or a portion of it? I’m interested in studying the contacts between subunits within the lattice. I know one could generate that using yeast tubulin dimers, but I don’t know exactly how. If someone has already done that and is willing to share it, that would be extremely helpful. Thanks a lot in advance, ciao, S PS: sorry for the cross posting to members of both bulletin boards. -- Sebastiano Pasqualato, PhD Biochemistry and Structural Biology Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

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Phenix-RSR model fit issue in CS-Map
by pramod kumar 23 Oct '19

23 Oct '19

Dear Experts, I have a map generated through cryosparc (ab initio-reconstr and homo-refine at 3.7A* FSC and sharpened in Scipion and separately in EMAN2). I have build the initial pdb through BALBES which has perfect validation parameters and nice fitting in the map (with the mtz output) but the co-ordinates are shifted from the true origin of CS-map. I used phenix-RSR to fit and refine, but validation results remained too far to accept the model as good solution and also a small region entered in wrong nearyby densities. So far following independent and downstream approaches I have taken:- In phenix; dock in map, map to model, rigid body refine followed by real space refine (with both .map and converted .mtz), using only chain A-map boxing and model generation through NCS. I have tried chimera fit for entire assembly and also only one chain in boxed map and full map but still the validation remained far from acceptable values and a small region in wrong neighboring density. Please help. -- Best regards, Promod

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errors in rosetta.refine
by Bram mylemans 18 Oct '19

18 Oct '19

dear I am trying to run rosetta.refine but get an error. I am using the latest version of phenix (1.17-3644) and I have tried to versions of rosetta (3.10 release date 2 Oct 2018 and 3.11 release date 26 Sept 2019) If I run rosetta.run_tests with rosetta 3.10 I get the following error message: DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: Segmentation fault (core dumped) If I run with rosetta 3.11 I get a different error message: DEBUG dumping error message ERROR: Rosetta exited with status 127 stderr output: /opt/rosetta_3.11_phenix/main/source/bin/rosetta_scripts.python.linuxgccrelease: error while loading shared libraries: libcifparse.so: cannot open shared object file: No such file or directory Are these version of rosetta and phenix compatible?

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Small Molecule Discovery RFP - Deadline is October 28th
by Nick DeHaan 17 Oct '19

17 Oct '19

Hi PhenixBB, I thought this group might be interested in an academic research support program that helps identify new active compounds based on protein structure. The award provides investigators, postdocs, or grad students with approximately 72 small molecules predicted by machine learning to bind to their protein of interest. A few awards also provide in-kind support (with a value of up to $20k) for the assay work. Applications take ~30 minutes to complete, and >300 awards will be given out this cycle. Proposals are due by October 28th. You can find out more here: Website: www.atomwise.com/aims <http://bit.ly/31rz1B4> Infographic: http://www.atomwise.com/wp-content/uploads/2019/10/AIMS-Infographic-Stats_F… <http://bit.ly/31jRa3O> Flyer: http://www.atomwise.com/wp-content/uploads/2019/10/Atomwise-AIMS-Awards-Fly… <http://bit.ly/31nkVAI> Please feel free to reach out to me with any questions! Best regards, Nick Nick DeHaan, MsE *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

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Job opening: Scientist-I (Structural Biology) at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 17 Oct '19

17 Oct '19

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology. The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leido… Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. *Office/Courier*: 8560 Progress Drive, C1012, Frederick, MD 21701 *USPS mail*: Post Office Box B, ATRF-C1012, Frederick, MD 21702 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

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high B Factor after real space refinement against a cryoEM map
by Keda Zhou 17 Oct '19

17 Oct '19

Dear all, I am trying to do the real space refinement for my model against a 5.0 angstrom cryoEM map. All parameters look pretty good except the B factor. The mean of the B factor is close to 400. I am just wondering whether the low resolution makes the B factor this high. Does anyone have any idea or suggestion on the high B factor during real space refinement? Is it possible to reduce it? What is the actual meaning of this B factor? Thanks in advance. cody

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Two tenure-track faculty openings at Univ. of Missouri Biochemistry
by Tanner, John J. 14 Oct '19

14 Oct '19

Dear Colleagues, My department has two tenure-track faculty openings. Review of applications will begin on November 15, 2019. Click the link below for more information. https://biochem.missouri.edu/open-positions/ John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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file location changed
by Cygler, Miroslaw 14 Oct '19

14 Oct '19

Hi, In order to allow synchronization of files on my mac with the cloud server I had to move all files used by Phenix to a new directory, including the main Phenix folder. How do I change the paths to these files in phenix so that they are accessible to the software? Phenix would not start without the main Phenix folder returned back to the old location. How do I rectify this as well? Thanks for your help, Mirek

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advert for PostDoc position @Singapore
by SR Bharath 14 Oct '19

14 Oct '19

Dear Colleagues, We are seeking an enthusiastic and self-motivated postdoctoral research fellow to study proteins involved in maintaining genome stability and the Hippo signaling pathway. We take a combinatorial approach of molecular biology, biochemical and biophysical methods, and structural biology (macromolecular crystallography and electron cryomicroscopy). Significant aspects of our projects have translational potential. The candidate is expected to be involved in the development of small molecules/peptides for cancer therapeutics. Singapore is an excellent environment to do research with many research groups close by in Biopolis [https://www.a-star.edu.sg/imcb]. A*STAR offers highly competitive salaries with benefits including housing allowance and 1-3 months performance bonus. Requirements: · PhD in biochemistry, biophysics, molecular & cell biology or in medicinal chemistry · Practical experiences in structural biology (Electron Cryomicroscopy and/or X-ray crystallography) or in medicinal chemistry · Good publication record · Competent in scientific writing Interested applicants should send a CV and three confidential letters of reference to: Prof. Haiwei Song (Email: *haiwei(a)imcb.a-star.edu.sg <https://webmail2.imcb.a-star.edu.sg/owa/redir.aspx?C=EzRllkOmnk2jjotDLR8t5a…>*), Institute of Molecular and Cell Biology, A*STAR, Singapore. Cheers, Bharath

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Masked FSC estimation failure
by ze li 12 Oct '19

12 Oct '19

Hello: I have three cryo-ET full maps, not in halves, to estimate their resolutions. I intended to estimate the resolution of the maps with the high-resolution models in the PDB databank. Is it the best to get a map to model FSC estimation at 0.5 cut-off? I calculated three maps with cryo-EM module in Phenix, but only one gives the masked and unmasked curves, the other two only have the unmasked results.I tried many times but failed to figure out the questions of these two maps. What is the possible reason for them? Or Is there any other ways to get the unmasked and masked FSC? Thank you for your help. Sincerely, Ze

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Berkeley Server Outage (Starting October evening 8th)
by Paul Adams 12 Oct '19

12 Oct '19

Dear Colleagues, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this week meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down today and will return later in the week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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University of Maryland/Open-Rank Tenure-Line Faculty Position
by Hasan, Syed Saif 09 Oct '19

09 Oct '19

Dear Colleagues, The Institute for Bioscience & Biotechnology Research (IBBR) and the University of Maryland, College Park Department of Chemistry & Biochemistry invite applications for an open-rank, tenure-line faculty position in structural biology, with an emphasis in the area of biomolecular cryo-electron microscopy, starting August 2020. A detailed ad is attached to this email. Applications, consisting of a cover letter, curriculum vitae, statement of research plans, statement of educational interests, and three references, must be submitted electronically at: https://ejobs.umd.edu/postings/74094 Review of applications will begin November 15, 2019. We will continue to accept applications until the position is filled. Direct inquiries and/or nominations to the chair of the search committee, at: cryoemsearch(a)ibbr.umd.edu Saif S. Saif Hasan, PhD https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/ https://www.ibbr.umd.edu/profiles/s-saif-hasan

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positional restraints in real_space_refine?
by Daniel Larsson 08 Oct '19

08 Oct '19

Hi all, I'm working on a cryo-EM reconstruction where I have some flexible low-resolution elements (RNA double helices). They have different orientations relative to my reference model, but I would like to model them in the approximately correct position. I've tried real_space_refine with morphing and simulated annealing, but neither accomplish what I want. Now I'm thinking of cutting out these helices and manually position them approximately where I want them. But I fear that this will case headache at the "joint". Is it possible to use the manual positions as a reference for positional restraints, but use the original model as the reference for the torsion angles. Is this possible with real_space_refine? Or is there a better way of refining this structure? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Phenix 1.17-3644 installation problems
by Hernando J Sosa 07 Oct '19

07 Oct '19

Dear Phenix developers, Trying to install Phenix in a Linux computer (OpenSuse Leap 15.1)I got the error messages listed below. Any help to fix this problem(s) would be appreciated. Thks. H. Precompiling .py files... Generating SOLVE/RESOLVE license file... Rebuilding HTML documentation... Error rebuilding documentation! Creating rotamer/Ramachandran database files... Traceback (most recent call last): File "./bin/install.py", line 244, in <module> installer(sys.argv[1:]).install() File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 201, in install self.install_finalize() File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 542, in install_finalize self.product_specific_finalize_install(log) File "./bin/install.py", line 130, in product_specific_finalize_install call([os.path.join(self.build_dir, 'bin', 'mmtbx.rebuild_rotarama_cache')], log=log) File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/home/hsxx/Programs/Phenix/phenix-1.17-3644/build/bin/mmtbx.rebuild_rotarama_cache' failed with exit code -4

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reference torsion restraints for nucleic acids in real_space_refine
by Daniel Larsson 07 Oct '19

07 Oct '19

Hi all, In phenix.real_space_refine, I'm using a reference model for torsion restraints for a RNA/protein complex. I noticed in the log file under the section "Adding Reference Model Restraints (torsion)" that only the amino acid residues and some modified nucleotides are listed in the "Reference Model Matching Summary" but not the standard nucleotides. Does this mean that they are not restrained? I checked the _initial.geo file and there are no torsion restraints for the standard nucleotides in the "Reference torsion angle restraints" section. Are they not supported by default? My workflow was this: run ready_set on the initial model and then supply real_space_refine with a reference model and the ready_set cif file with the ligands. Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Base-pair restraints and high resolution cryoEM maps
by Stephen Cusack 07 Oct '19

07 Oct '19

Dear All, (1) Is it possible to add RNA base-pair restraints into Phenix Real-space-refinement of a lowish resolution cryoEM structure? If so how? (2) We are also lucky enough to have some impressively high resolution cryoEM maps (2.4 A average) which show among other things hundreds of water molecules. I was wondering whether Phenix Real-space-refinement was really adapted to high resolution, e.g. it uses grouped B-factor refinement and has no water handling options (putting them in manually is a pain and you always miss some). How have other people dealt with these issues ? thanks for any help Stephen Cusack -- ********************************************************************** Dr. Stephen Cusack, FRS Head of EMBL Grenoble Group leader in the structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr, stephen.cusack(a)embl.org Website: http://www.embl.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 Fax: (33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

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PhD and postdoc position - Structural Biology Methods development at Wuerzburg University
by Andrea Thorn 07 Oct '19

07 Oct '19

Dear colleagues, for two projects in structural biology methods development, we are looking for a PHD CANDIDATE (m/f/d) and a POSTDOCTORAL RESEARCHER (m/f/d) The Thorn Laboratory the Rudolf Virchow Center at the University of Wuerzburg develops new methods for macromolecular X-ray crystallography and Cryo-EM. In these exciting projects you will improve how well we understand, measure and model macromolecular crystal structures using practical experiments and big data analyses. We are looking for candidates with skills in data analysis and programming. Any previous experiences in crystallography, molecular biology, machine learning, image or statistical analysis are also a bonus. You should be a good communicator. For the PhD project, we offer a 36-month full- or part-time position, embedded in the Würzburg Graduate School for Life Sciences (GSLS); for the postdoctoral position, we offer a 30-month full- or part-time position with a competitive salary as well as career and family support. Women are particularly encouraged to apply. For more details, see: https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_PhD_Tho… https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_Postdoc… If you have any questions, please email me: andrea.thorn(a)uni-wuerzburg.de. Best wishes, Andrea Thorn. _____ Dr. Andrea Thorn group leader Rudolf Virchow Center for Experimental Biomedicine University of Wuerzburg Josef-Schneider-Str. 2 97080 Wuerzburg Germany andrea.thorn(a)uni-wuerzburg.de https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/tho…

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Position Available: Crystallography Facility Manager (Research Assistant Professor) - CUNY Advanced Science Research Center, New York City
by Keedy, Daniel 03 Oct '19

03 Oct '19

To the phenixbb community, The Structural Biology Initiative ( https://asrc.gc.cuny.edu/structbio ) of the CUNY Advanced Science Research Center has an available position for an X-ray Crystallography Facility Manager (Research Assistant Professor) starting immediately. The CUNY Advanced Science Research Center is a new cutting-edge research institution located in New York City, bringing together five Initiatives whose research areas span many length scales: Structural Biology, Nanoscience, Photonics, Neuroscience, and Environmental Science. The Structural Biology Initiative (SBI) features seven tenure-track and research faculty members, pursuing research problems across biological and chemical topics using techniques as diverse as X-ray diffraction, cryo-EM, NMR, solution biophysics, and advanced microscopy. The SBI also hosts state-of-the-art core facilities in three different areas: nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and X-ray crystallography. The Structural Biology Initiative seeks a Facility Manager/Research Assistant Professor for the X-ray Macromolecular Crystallography Facility, which is already equipped with a Rigaku Alchemist DT liquid handler, two ARI Gryphon crystallization robots, and two Rigaku Minstrel DT crystal imagers at room temperature and 4°C. The selected candidate will be responsible not only for directing day-to-day operations of the facility in concert with users from the ASRC and externally, but also for developing an independent research program that leverages emerging technologies in X-ray crystallography. The ASRC is located in upper Manhattan, immediately adjacent to the New York Structural Biology Center (NYSBC), a consortium of CUNY and eight other New York academic institutions with world-class cryo-EM, NMR, and X-ray facilities on-site and at Brookhaven National Laboratory. BNL, located just 70 miles from the ASRC, includes a newly constructed synchrotron, National Synchrotron Light Source II, which opened in 2015. NSLS-II is now the brightest synchrotron light source in the United State, offering X-rays that are 10,000x brighter than the original NSLS. The ASRC Structural Biology Initiative has access to several cutting-edge microfocus beamlines equipped for automated crystal handling and data collection at NSLS-II, including the NYX beamline via CUNY’s membership in NYSBC and the AMX and FMX beamlines via proposals. Please find more detailed information about the position and officially apply via the following URL: https://cuny.jobs/new-york-ny/macromolecular-crystallization-facility-manag… Review of applications will begin on October 16. Best regards, Daniel Keedy — Daniel A. Keedy, Ph.D. Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry and Chemistry Ph.D. Programs, CUNY Graduate Center www.keedylab.org<http://www.keedylab.org> | dkeedy(a)gc.cuny.edu<mailto:[email protected]> (NOT @asrc) | 212-413-3246

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Re: [phenixbb] Figure of merit from refinement
by Alexandre OURJOUMTSEV 03 Oct '19

03 Oct '19

Dear Andre, (I repeat here the same message that I've just sent through the ccp4bb; sorry for answering late) I would strongly advice you to look at the article by Lunin and Skovoroda (Acta Cryst, A, 1995) that addresses exactly your question: https://scripts.iucr.org/cgi-bin/paper?vs0124 The authors remind a very important point that after model refinement ML phase errors are strongly underestimated if using all reflections, as that was done in the original works (see references in the article). While the same ML estimates work perfectly for unrefined models, that's not the case for refined ones, as was observed yet in the beginning of 80ths. These authors show then that using the test-set of reflections (the same as for R-free) is crucial to get the correct phase error estimates and respective FOMs for all cases, as this is implemented now in modern refinement programs, e.g. phenix.refine. See also the article by Pannu & Read (Acta Cryst, A, 1996) https://onlinelibrary.wiley.com/doi/pdf/10.1107/S0108767396004370 A more recent important article on this topic is that by Praznikar and Turk (Acta Cryst, D, 2009) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257616/ who discuss what can be done if a statistically significant test set of reflections is not available. I hope this helps you. I am ready to answer you further eventual questions (probably, in a private correspondence). With best wishes, Sacha Urzhumtsev ________________________________ -------- Forwarded Message -------- Subject: [phenixbb] Figure of merit from refinement Date: Tue, 1 Oct 2019 08:15:14 -0300 From: Andre LB Ambrosio <andre(a)ifsc.usp.br><mailto:[email protected]> To: phenixbb(a)phenix-online.org<mailto:[email protected]> Dear all, How is the FOM calculated for a given reflection specifically in the context of model refinement? How useful is it in assessing the phase quality, when not for initial experimental phases? Many thank in advance, -- Andre LB Ambrosio

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Figure of merit from refinement
by Andre LB Ambrosio 01 Oct '19

01 Oct '19

Dear all, How is the FOM calculated for a given reflection specifically in the context of model refinement? How useful is it in assessing the phase quality, when not for initial experimental phases? Many thank in advance, -- Andre LB Ambrosio

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General interest
by John R Helliwell 30 Sep '19

30 Sep '19

Dear Colleagues, I draw your attention to my posting at the IUCr Committee on Data Public Forum ( https://forums.iucr.org/viewtopic.php?f=39&t=423 ) about the recent USA National Academies Report on Reproducibility and Replicability in Science. Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data

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Final reminder: MicroED Workshop 2019
by Johan Hattne 30 Sep '19

30 Sep '19

Final reminder: the application deadline for the 2019 MicroED workshop is October 1, 2019. From the initial announcement: The Gonen Laboratory will hold the 5th MicroED Workshop in 2019. The workshop will be held at the MicroED Imaging Center at the UCLA David Geffen School of Medicine during December 9-12, 2019 and is open to both academia and industry. Space is limited and historically, the workshop is typically oversubscribed. Topics covered: * MicroED conception, practice, and future opportunities * Electron optics for MicroED * Microscope alignment and calibration for MicroED * Sample preparation: protein and organic/inorganic materials, small molecules * Data collection for both protein and small molecules * Data analysis software, structure solution, and refinement * Choice of electron microscope hardware and cameras * MicroED publication standards: what statistics to include and when is your structure publication-ready? Further application information is available from https://cryoem.ucla.edu/pages/Workshop // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095

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What OS do you use?
by Murpholino Peligro 22 Sep '19

22 Sep '19

I want to know what operating system you use. For that I made a poll, it is anonymous, quite simple and plus you get to see the results. (link https://forms.gle/7VT4pgbHQQmeAvpp8) I hope you contribute. Thanks

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Potential Berkeley Server Outage (September 23/24)
by Paul Adams 21 Sep '19

21 Sep '19

Dear Colleagues, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. They are predicting that Monday or Tuesday this coming week (September 23/24) might meet their criteria for a shutdown in the Bay Area. Hopefully this is just a worst case prediction and nothing will happen. However, there is a possibility that the Berkeley servers will be down for some time during that period (duration unknown). This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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